On Sunday 29 August 2004 06:37 pm, tarek mahfouz wrote:
> Dear Amber users,
> Can anyone tell me how to make LEaP understand that I want neutral N and
> C termini? or if I wanted to add acetyl or N-methylamino groups, how to
> do this? Thanks,
> Tarek
> .
>

Read the section on amino acid residues. (3.5.2 in the amber8 pdf
documentation, available on the amber web site if you do not have
amber8. I don't think this part has changed since LEaP was
introduced.) For example, if the n-term is ALA, and you want it
to be uncharged, you will have to develop an uncharged N-terminal
ALA residue using the standard methods for new residue
definitions. (Unless uncharged N-terminal residues have been
introduced in some of the newer force fields.) Developing a new
residue definition, given a structure, involves a quantum chemical
calculation of the electrostatics followed by an atom-based charge
assignment with resp. The whole procedure can be automated with
RED (see the amber web site).

The regular ALA is an internal residue, and as such the amine only
has one hydrogen. NALA would be the positively charged (ordinary)
n-term residue. Similarly for the other aa's. The beginning
acetyl and ending N-methylamine, etc are also defined in this
section.

You define a sequence using a list. The example given is

x = { ALA VAL SER PHE }

then use loadPdbUsingSeq to load a pdb file and ensure the correct
residue definitions are used. (E.g., HID or HIE for the delta or
epsilon protonated histidine.) In particular, x as defined above
would not have proper protein N- and C-termini.

x = { NALA VAL SER CPHE }

would have charged termini.

If you are going to develop new residues, I suggest you thoroughly
familiarize yourself with the LEaP documentation as well as the
original literature for the AMBER force fields. Also read the
manuals for antechamber and resp, although antechamber is not
itself directly applicable to the development of new monomeric
residue definitions for biopolymers.